Firstly, I apologise if I have misunderstood or I have looked in the wrong place for this.

When a user disables an application and still wishes to proceed with changing setting or adding new content etc, there is no way to access the application without re-enabling it. Why is the end user restricted in this manner or, as I have already said, maybe I am missing something here?

A prime example. If I wish to install another menu system, I would like to have the ability to 'set' it up first before switching over, or I risk my members having no menu system while I 'tinker' about with the new one.

just set the permissions for who can use the app. leave it enabled. if they cant use it they cant see it.